The rebel Free Syrian Army (FSA) has been accused of repeated abuses of regime loyalists.
Opposition fighters have allegedly tortured, kidnapped and executed security force members and civilians.
In recent days, there have been reports of bodies being thrown from rooftops and the beheading of a government soldier.
Arif al-Hummoud, a senior commander in the FSA based in Turkey, said the brutality of the Syrian government forces had triggered some rebels to take the law into their own hands, carrying out rights violations.
"We as the generals and the commanders of the FSA condemn these actions," he said.
Hummoud also said that the FSA lacks a central leadership and is not in control of all the fighting units on the ground.
In March, Human Rights Watch issued a statement condemning the rebels for carrying out the same kind of abuses as the Syrian government.